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Your problem is probably related to pixel aspect ratio. That's the aspect ratio most folks don't know about, or forget about.
Sounds like the PAR is slightly not square. With the right tools you can determine if the PAR is 1:1.00000, or something else.
Also sounds like all the other FLV encoders were all based on FFmpeg. If so, that would account for the same errors you got. Where FFmpeg gets its PAR information probably depends on the specific codec you used. FFmpeg is known to get it wrong sometimes, but if you use the command-line interface to it, you can tweak just about anything.
In any case, don't use FFmpeg anyway. It encodes to a very old, and now obsolete, FLV format. You want FLV VP6. You get that with Adobe Media Encoder, On2 Flix, and Sorenson Squeeze.
Say after me: ALL FFMPEG-BASED FLV ENCODERS PRODUCE CRAP.
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